A method for breeding a first filial generation is also called a method for breeding of a hybrid-variety. This method is utilized in variety-breeding since a variety having excellent traits inherited from its parents and showing heterosis hybrid vigour can be bred by means of this method. In order to economically harvest F1 hybrid seeds in large quantity, a three-line method utilizing cytoplasmic male sterility is adopted in the case of seed-harvesting of a hybrid variety of rice. The three-line method refers to a method that utilizes a sterile line having male sterility, a fertility restorer line, and a maintainer line having the same nuclear genes as the sterile line but not having sterile cytoplasm. According to this three-line method, (1) a hybrid seed can be harvested by crossing the sterile line with pollen of the restorer line, while (2) the sterile line can be maintained by crossing the sterile line with the pollen of the maintainer line.
BT-type male sterile cytoplasm and WA-type male sterile cytoplasm have been used worldwide in order to breed the hybrid variety with the three-line method. On the other hand, CW-type male sterile cytoplasm has been hardly utilized since the structure and function of a fertility restorer gene Rf17 (Non Patent Document 1) have not been clarified. However, since there may be a risk of variety collapse due to limit in the genetic resources provided by the male sterile cytoplasm that have been used until now, utilization and development of novel male sterile cytoplasm are now desired.
In the prior arts, it has been necessary to breed plant body (F1) from a hybrid seed obtained by test cross, and then to make the F1 self-cross and to investigate frequency of appearance of a individual plant having seed-development rate over a certain level (for example, 90% or more) for the estimation of a genotype of Rf17 locus in the plant. It has not been possible to determine said genotype by means of DNA markers.    Non Patent Document 1: Sota Fujii and Kinya Toriyama (2005) Molecular mapping of the fertility restorer gene for ms-CW-type cytoplasmic male sterility of rice. Theor. Appl. Genet. 111:696-701